Ion channels in the KCNH family perform diverse and important physiological functions, including the regulation of cancer progression, neuronal excitability and cardiac contraction. KCNH channels contain a Per-Arnt-Sim (PAS) domain in their N-terminal and cyclic nucleotide-binding homology (CNBH) domain in their C-terminal regions. These intracellular domains are the key functional domains that are largely responsible for the distinct properties of KCNH channels that determine their physiological applications. The goal of this proposal is to identify small molecule ligands that directly bind to the PAS and CNBH domains and uncover the mechanisms of their action on KCNH channels. We will identify and functionally characterize KCNH channel ligands using a novel strategy based on the combination of surface plasmon resonance (SPR) and electrophysiology as the principal methods. We will first identify small molecule ligands by screening libraries of small molecules against the PAS and CNBH domains of KCNH channels with the high-throughput SPR method. We will then determine the functional effects of the identified small molecule ligands with medium-throughput two- electrode voltage-clamp method. Finally to uncover molecular mechanisms of action of the identified ligands we will use a combination of patch-clamp current recordings, mutagenesis, X-ray crystallography, SPR and structural modeling. These studies will advance our knowledge of KCNH channel regulation by intracellular ligands and PAS and CNBH domains, provide pharmacological tools to study physiological contributions of KCNH channels and will greatly facilitate the development of novel pharmaceutical agents for treatment of cardiac arrhythmias, cancer and epilepsy.